Code: Select all
[08:12:00]
[08:12:00] *------------------------------*
[08:12:00] Folding@Home Gromacs SMP Core
[08:12:00] Version 2.07 (Sun Apr 19 14:51:09 PDT 2009)
[08:12:00]
[08:12:00] Preparing to commence simulation
[08:12:00] - Ensuring status. Please wait.
[08:12:09] - Looking at optimizations...
[08:12:09] - Working with standard loops on this execution.
[08:12:09] - Files status OK
[08:12:10] - Expanded 4834945 -> 24033949 (decompressed 497.0 percent)
[08:12:10] Called DecompressByteArray: compressed_data_size=4834945
data_size=24033949, decompressed_data_size=24033949 diff=0
[08:12:10] - Digital signature verified
[08:12:10]
[08:12:10] Project: 2671 (Run 32, Clone 80, Gen 41)
[08:12:10]
[08:12:11] Entering M.D.
NNODES=8, MYRANK=0, HOSTNAME=computenode
NNODES=8, MYRANK=1, HOSTNAME=computenode
NNODES=8, MYRANK=3, HOSTNAME=computenode
NNODES=8, MYRANK=4, HOSTNAME=computenode
NNODES=8, MYRANK=5, HOSTNAME=computenode
NNODES=8, MYRANK=6, HOSTNAME=computenode
NNODES=8, MYRANK=7, HOSTNAME=computenode
NNODES=8, MYRANK=2, HOSTNAME=computenode
NODEID=0 argc=20
NODEID=1 argc=20
NODEID=4 argc=20
NODEID=5 argc=20
NODEID=6 argc=20
NODEID=7 argc=20
NODEID=2 argc=20
NODEID=3 argc=20
:-) G R O M A C S (-:
Groningen Machine for Chemical Simulation
:-) VERSION 4.0.99_development_20090307 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.
:-) mdrun (-:
Reading file work/wudata_06.tpr, VERSION 3.3.99_development_20070618 (single
precision)
Note: tpx file_version 48, software version 64
NOTE: The tpr file used for this simulation is in an old format, for less memory
usage and possibly more performance create a new tpr file with an up to date
version of grompp
Making 3D domain decomposition 2 x 2 x 2
starting mdrun '22908 system in water'
10500000 steps, 21000.0 ps (continuing from step 10250001, 20500.0 ps).
[08:12:20] Completed 0 out of 249999 steps (0%)
[08:16:44] Completed 2500 out of 249999 steps (1%)
[08:21:07] Completed 5000 out of 249999 steps (2%)
[08:25:30] Completed 7500 out of 249999 steps (3%)
[08:29:53] Completed 10000 out of 249999 steps (4%)
[08:34:16] Completed 12500 out of 249999 steps (5%)
[08:38:39] Completed 15000 out of 249999 steps (6%)
[08:43:04] Completed 17500 out of 249999 steps (7%)
[08:47:31] Completed 20000 out of 249999 steps (8%)
[08:51:58] Completed 22500 out of 249999 steps (9%)
[08:56:24] Completed 25000 out of 249999 steps (10%)
[09:00:51] Completed 27500 out of 249999 steps (11%)
[09:05:18] Completed 30000 out of 249999 steps (12%)
[09:09:45] Completed 32500 out of 249999 steps (13%)
[09:14:12] Completed 35000 out of 249999 steps (14%)
[09:18:39] Completed 37500 out of 249999 steps (15%)
[09:23:06] Completed 40000 out of 249999 steps (16%)
[09:27:32] Completed 42500 out of 249999 steps (17%)
[09:31:59] Completed 45000 out of 249999 steps (18%)
[09:36:26] Completed 47500 out of 249999 steps (19%)
[09:40:53] Completed 50000 out of 249999 steps (20%)
[09:45:20] Completed 52500 out of 249999 steps (21%)
[09:49:46] Completed 55000 out of 249999 steps (22%)
[09:54:13] Completed 57500 out of 249999 steps (23%)
[09:58:40] Completed 60000 out of 249999 steps (24%)
[10:03:06] Completed 62500 out of 249999 steps (25%)
[10:07:33] Completed 65000 out of 249999 steps (26%)
[10:11:59] Completed 67500 out of 249999 steps (27%)
[10:16:26] Completed 70000 out of 249999 steps (28%)
[10:20:53] Completed 72500 out of 249999 steps (29%)
[10:25:19] Completed 75000 out of 249999 steps (30%)
[10:29:46] Completed 77500 out of 249999 steps (31%)
[10:34:13] Completed 80000 out of 249999 steps (32%)
[10:38:40] Completed 82500 out of 249999 steps (33%)
[10:43:08] Completed 85000 out of 249999 steps (34%)
[10:47:35] Completed 87500 out of 249999 steps (35%)
[10:52:03] Completed 90000 out of 249999 steps (36%)
[10:56:30] Completed 92500 out of 249999 steps (37%)
[11:00:57] Completed 95000 out of 249999 steps (38%)
[11:05:24] Completed 97500 out of 249999 steps (39%)
[11:09:51] Completed 100000 out of 249999 steps (40%)
[11:14:18] Completed 102500 out of 249999 steps (41%)
[11:18:45] Completed 105000 out of 249999 steps (42%)
[11:23:12] Completed 107500 out of 249999 steps (43%)
[11:27:40] Completed 110000 out of 249999 steps (44%)
[11:32:06] Completed 112500 out of 249999 steps (45%)
[11:36:33] Completed 115000 out of 249999 steps (46%)
[11:41:00] Completed 117500 out of 249999 steps (47%)
[11:45:27] Completed 120000 out of 249999 steps (48%)
[11:49:54] Completed 122500 out of 249999 steps (49%)
[11:54:21] Completed 125000 out of 249999 steps (50%)
[11:58:48] Completed 127500 out of 249999 steps (51%)
[12:03:15] Completed 130000 out of 249999 steps (52%)
[12:07:42] Completed 132500 out of 249999 steps (53%)
[12:12:09] Completed 135000 out of 249999 steps (54%)
[12:16:38] Completed 137500 out of 249999 steps (55%)
[12:21:04] Completed 140000 out of 249999 steps (56%)
[12:25:31] Completed 142500 out of 249999 steps (57%)
[12:29:59] Completed 145000 out of 249999 steps (58%)
[12:34:25] Completed 147500 out of 249999 steps (59%)
[12:38:51] Completed 150000 out of 249999 steps (60%)
[12:43:16] Completed 152500 out of 249999 steps (61%)
[12:47:40] Completed 155000 out of 249999 steps (62%)
[12:52:04] Completed 157500 out of 249999 steps (63%)
[12:56:28] Completed 160000 out of 249999 steps (64%)
[13:00:53] Completed 162500 out of 249999 steps (65%)
[13:05:17] Completed 165000 out of 249999 steps (66%)
A list of missing interactions:
Angle of 42219 missing 1
Ryckaert-Bell. of 53121 missing 2
LJ-14 of 60948 missing 3
exclusions of 250194 missing 4
Molecule type '22908 system in water'
the first 10 missing interactions, except for exclusions:
Ryckaert-Bell. atoms 6851 6853 6855 6857 global 6851 6853 6855 6857
LJ-14 atoms 6851 6857 global 6851 6857
Angle atoms 6853 6855 6857 global 6853 6855 6857
Ryckaert-Bell. atoms 6854 6853 6855 6857 global 6854 6853 6855 6857
LJ-14 atoms 6854 6857 global 6854 6857
LJ-14 atoms 6857 6859 global 6857 6859
-------------------------------------------------------
Program mdrun, VERSION 4.0.99_development_20090307
Source code file: domdec_top.c, line: 350
Fatal error:
10 of the 459744 bonded interactions could not be calculated because some atoms
involved moved further apart than the multi-body cut-off distance (1.2 nm) or the
two-body cut-off distance (1.2 nm), see option -rdd, for pairs and tabulated
bonds also see option -ddcheck
For more information and tips for trouble shooting please check the GROMACS Wiki
at
http://wiki.gromacs.org/index.php/Errors
-------------------------------------------------------
Thanx for Using GROMACS - Have a Nice Day
Error on node 0, will try to stop all the nodes
Halting parallel program mdrun on CPU 0 out of 8
gcq#0: Thanx for Using GROMACS - Have a Nice Day
[cli_0]: aborting job:
application called MPI_Abort(MPI_COMM_WORLD, -1) - process 0
[cli_4]: aborting job:
Fatal error in MPI_Sendrecv: Error message texts are not available
[0]0:Return code = 255
[0]1:Return code = 0, signaled with Quit
[0]2:Return code = 0, signaled with Quit
[0]3:Return code = 0, signaled with Quit
[0]4:Return code = 1
[0]5:Return code = 0, signaled with Quit
[0]6:Return code = 0, signaled with Quit
[0]7:Return code = 0, signaled with Quit
[13:09:31] CoreStatus = FF (255)
[13:09:31] Sending work to server
[13:09:31] Project: 2671 (Run 32, Clone 80, Gen 41)
[13:09:31] - Error: Could not get length of results file work/wuresults_06.dat
[13:09:31] - Error: Could not read unit 06 file. Removing from queue.
[13:09:31] Trying to send all finished work units
[13:09:31] + No unsent completed units remaining.
[13:09:31] - Preparing to get new work unit...
[13:09:31] + Attempting to get work packet
[13:09:31] - Will indicate memory of 16003 MB
[13:09:31] - Connecting to assignment server
[13:09:31] Connecting to http://assign.stanford.edu:8080/
[13:09:36] Posted data.
[13:09:36] Initial: 43AB; - Successful: assigned to (171.67.108.24).
[13:09:36] + News From Folding@Home: Welcome to Folding@Home
[13:09:36] Loaded queue successfully.
[13:09:36] Connecting to http://171.67.108.24:8080/
[13:09:43] Posted data.
[13:09:43] Initial: 0000; - Receiving payload (expected size: 4835457)
[13:09:53] - Downloaded at ~472 kB/s
[13:09:53] - Averaged speed for that direction ~413 kB/s
[13:09:53] + Received work.
[13:09:53] Trying to send all finished work units
[13:09:53] + No unsent completed units remaining.
[13:09:53] + Closed connections
[13:09:58]
[13:09:58] + Processing work unit
[13:09:58] Core required: FahCore_a2.exe
[13:09:58] Core found.
[13:09:59] Working on queue slot 07 [June 2 13:09:59 UTC]
[13:09:59] + Working ...
[13:09:59] - Calling './mpiexec -np 8 -host 127.0.0.1 ./FahCore_a2.exe -dir work/
-suffix 07 -checkpoint 15 -verbose -lifeline 16939 -version 624'